In situ estimation of coral recruitment patterns from shallow to mesophotic reefs using an optimized fluorescence imaging system 
Hagai Nativ1,2, Federica Scucchia1,3, Stephane Martinez1,2, Shai Einbinder1,2, Alex Chequer4, Gretchen Goodbody-Gringley4, Tali Mass1,2
1Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
2Morris Kahn Marine Research Station, The Leon H. Charney School of Marine Sciences, University of Haifa, Sdot Yam, Israel
3The Interuniversity Institute of Marine Sciences, Eilat, Israel
4Central Caribbean Marine Institute, Little Cayman, Cayman Islands
This electronic notebook provides the raw data employed to analyze coral recruitment dynamics across shallow and mesophotic reefs of the northern Red Sea and Bermuda.
Coral recruitment represents a key element for coral reef persistence and resilience in the face of environmental disturbances. Studying coral recruitment patterns is fundamental for assessing reef health and implementing appropriate management strategies in an era of climate change. The FluorIS system has been developed to acquire high resolution, wide field-of-view (FOV) in situ images of coral recruits fluorescence and has proven successful in shallow reef environments. However, up to now, its applicability to mesophotic coral ecosystems remains unknown due to the complexity of the system and the limited time available when working at mesophotic depth. In this study we optimized the FluorIS system by utilizing a single infrared-converted camera instead of the bulkier regular dual-camera system, substantially reducing the system complexity and significantly decreasing the acquisition time to an average of 10 seconds for a set of 3 images. Moreover, the speed-FluorIS system is much more economical, decreasing the cost of the full set-up by roughly 40% compared to the original dual-camera system. We tested the utility of the speed-FluorIS by surveying coral recruits across shallow and mesophotic reefs of the Red Sea (Gulf of Eilat) and Bermuda, two of the most northerly reefs in the world with markedly different substrate and topography, and demonstrate that the modified system enables fast imaging of fluorescence to study coral recruitment patterns over a broader range of depths and reef topographies than previous fluorescence methods. Our single-camera system represents a valuable, non-invasive and rapid underwater tool which will help standardize surveys and long-term monitoring of coral recruits, contributing to our understanding of these vital and delicate early life stages of corals.
Raw fluorescence images - Raw images taken in Eilat at 5 meters and 45 meters, and in Bermuda at 5 meters and 45 meters.
Coral recruits count - Raw data of coral recruits count based on the fluorescence images.
Workflow video - Video describing the workflow of the image processing.